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We cannot connect to schema manager using system/manager anymore it says that table or view does not exists .. I can connect to it using worksheet.
when I look at dba_tablespaces it shows default tablespace for SYSTEM as USER. Is it correct ??? Should that be SYSTEM.
I can connect to it using sys/password.

I don't know what has happened but SYSTEM user and all other users had lost priviledges to user tables and v$objects. After I ran catalog.sql script everthing seems to be fine now.
I cnhanged sys password before that could that cause this ??
One more thing in catalog.sql script...
create or replace view v_$dlm_latch as select * from v$dlm_latch;
drop public synonym v$dlm_latch;
create public synonym v$dlm_latch for v_$dlm_latch;
grant select on v_$dlm_latch to select_catalog_role;

I had to change 'select_catalog_role' with 'dba' to get everything back to working. Why 'select_catalog_role' did not work ?

How come I was able to view all these views and connect to schema manager using sys access ? Why not system..
I even tries grant execute and select on these catalog objects to system. It did not work.

possibly something happened to your select_catalog_role. sys owns the objects so he doesn't need the role to be able to see them. what error did it give that let you know that select_catalog_role wasn't working?